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As for the monetisation of the pligg, I think on most pages the advertising should be very light, and only on the actual story pages you could have large ads area between the header and the content.
I think often the traffic from search engine will come on specific story pages (and categories page too) so you can display big ads. But for the regular users, most of the interface should be light in ads, so they are not put off by them.
My suggestions are that top right spot, in the sidebar, a 250x250 ad. And also just below the header/navbar or at the top of the content senction, if you can put something thin like an adsense link units, 728x15
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